DNA barcoding will frequently fail in complicated groups: An example in wild potatoes

Spooner, David M.

doi:10.3732/ajb.0800246

Cited by 162 publications

(161 citation statements)

References 109 publications

(138 reference statements)

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“…DNA-based identification (barcoding) is simple, does not require taxonomic expertise, and is free from subjective errors, which is not the case in morphological identification. Valid identification of unknown samples is the main goal of barcoding (Hebert and Gregory, 2005), despite ongoing criticism of the feasibility or even necessity of DNA barcoding for general taxonomic purposes Spooner, 2009). Nowadays, it is widely accepted that any valid plant barcode should be multi-locus, preferably comprising a conserved coding region such as rbcL and a more rapidly evolving region that is most likely non-coding (Kress et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

DNA barcoding of arid wild plants using rbcL gene sequences

Bafeel¹,

Arif²,

Bakir³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. DNA barcoding is currently gaining popularity due to its simplicity and high accuracy as compared to the complexity and subjective biases associated with morphology-based identification of taxa. The standard chloroplast DNA barcode for land plants recommended by the Consortium for the Barcode of Life (CBOL) plant working group needs to be evaluated for a wide range of plant species. We therefore tested the potential of the rbcL marker for the identification of wild plants belonging to diverse families of arid regions. Maximum likelihood tree analysis was performed to evaluate the discriminatory power of the rbcL gene. Our findings showed that using rbcL gene sequences enabled identification of the majority of the samples (92%) to genus level and only 17% to species level.

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Section: Introductionmentioning

confidence: 99%

DNA barcoding of arid wild plants using rbcL gene sequences

Bafeel¹,

Arif²,

Bakir³

et al. 2012

Genet. Mol. Res.

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“…In some cases of complex recently evolved species groups DNA barcoding may simply be inappropriate as an identification tool (2). This difficulty is especially acute in cases where certain life history traits have affected the rates of molecular evolution in a lineage, which in turn may affect rates of species assignment by DNA barcodes [e.g., generation times (3) and age-of-crown group diversification (4)].…”

mentioning

confidence: 99%

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

Kress

Erickson

Jones

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

636

695

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The assembly of DNA barcode libraries is particularly relevant within species-rich natural communities for which accurate species identifications will enable detailed ecological forensic studies. In addition, well-resolved molecular phylogenies derived from these DNA barcode sequences have the potential to improve investigations of the mechanisms underlying community assembly and functional trait evolution. To date, no studies have effectively applied DNA barcodes sensu strictu in this manner. In this report, we demonstrate that a three-locus DNA barcode when applied to 296 species of woody trees, shrubs, and palms found within the 50-ha Forest Dynamics Plot on Barro Colorado Island (BCI), Panama, resulted in >98% correct identifications. These DNA barcode sequences are also used to reconstruct a robust community phylogeny employing a supermatrix method for 281 of the 296 plant species in the plot. The three-locus barcode data were sufficient to reliably reconstruct evolutionary relationships among the plant taxa in the plot that are congruent with the broadly accepted phylogeny of flowering plants (APG II). Earlier work on the phylogenetic structure of the BCI forest dynamics plot employing less resolved phylogenies reveals significant differences in evolutionary and ecological inferences compared with our data and suggests that unresolved community phylogenies may have increased type I and type II errors. These results illustrate how highly resolved phylogenies based on DNA barcode sequence data will enhance research focused on the interface between community ecology and evolution.T he most difficult challenge for DNA barcoding in plants is discriminating among taxa of highly speciose genera where rates of species identification by using a variety of putative barcodes rarely exceed 70% (1). In some cases of complex recently evolved species groups DNA barcoding may simply be inappropriate as an identification tool (2). This difficulty is especially acute in cases where certain life history traits have affected the rates of molecular evolution in a lineage, which in turn may affect rates of species assignment by DNA barcodes [e.g., generation times (3) and age-of-crown group diversification (4)].In the absence of a universal barcode region capable of discriminating among all species in all groups of plants, it is clear that DNA barcodes will be most effectively applied in the identification of a circumscribed set of species that occur together in a floristic region or ecological community, rather than in distinguishing among an exhaustive sample of taxonomically closely related species. In these cases only a limited number of closely related species occur in the same region, so identification to genus is all that is required.It is now generally agreed that a plant barcode will combine more than one locus (5-7) and will include a phylogenetically conservative coding locus (rbcL) with one or more rapidly evolving regions (part of the matK gene and the intergenic spacer trnH-psbA). Although more laborious than a si...

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“…However, species delimitation based on mitochondrial genes only may not reflect species boundaries as accurately as an integrative approach exploring a combination of various data sources (Will et al 2005;Spooner 2009;Dupuis et al 2012;Carstens et al 2013). Essentially, a multilocus strategy provides independent estimates of both mitochondrial and nuclear genealogical histories, and congruence among estimates provides strong evidence of actual species divergence.…”

Section: Introductionmentioning

confidence: 99%

Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae)

Liu

Fend²,

Martinsson

et al. 2017

Org Divers Evol

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Limnodrilus hoffmeisteri Claparède, 1862 is a common freshwater worm, often regarded as an indicator of organic pollution. The taxonomic status of this species is controversial due to great variation in morphological features. Numerous morphological forms of L. hoffmeisteri are recorded in the literature, especially from Europe and North America. Today, DNA-based species delimitation assumes that species boundaries can be more objectively and effectively estimated using genetic data rather than with morphological data alone. To investigate if L. hoffmeisteri is a single species, 295 worms identified as either L. hoffmeisteri or other similar (congeneric) morphospecies, using currently accepted morphological criteria, were collected from 82 locations in the northern hemisphere. The number of primary species hypotheses (PSHs) was first explored with cytochrome oxidase subunit I (COI), the proposed DNA barcode for animal species, and with data for all specimens. Both automatic barcoding gap discovery (ABGD) and the Bayesian general mixed Yule coalescent (bGMYC) model revealed the existence of ≥25 distinct PSHs (COI lineages) in our dataset. Then, smaller samples of individuals representing major COI lineages were used for exploration of a nuclear locus, the internal transcribed spacer (ITS) region. In the ITS gene tree (81 sequences), generated by BEAST, 16 well-supported terminal groups were found, but not all of these groups were congruent with the PSHs found in the COI tree. As results across these different analyses were inconsistent, we resorted to analyzing reciprocal monophyly between gene trees and used a minimum consensus of all evidence, suggesting that there are 13 separately evolving lineages (=13 species) within our sample. The smallest uncorrected COI p-distance between these species is 12.1%, and the largest intraspecific p-distance is 16.4%, illustrating the problem of species delimitation with a DNAbarcoding gap as the sole criterion. Ten of these species are morphologically identified as BL. hoffmeisteri,^the remaining three can be attributed to morphologically distinct congeneric species. An individual from the type locality in Switzerland was designated as a neotype of L. hoffmeisteri sensu stricto. This worm belongs to one of the ten species, and this lineage is widely distributed in Europe, Asia, and North America. The remaining nine species show a mixed distribution pattern; some appear to be endemic to a restricted area, others are Holarctic. Our results provide clues to the future revalidation of some of the nominal species today placed in synonymy with L. hoffmeisteri. A BEAST analysis, based on previously published and newly generated 16S data, suggested that this complex contains also other species than those studied by us. By integrating additional genetic data, it will be possible to identify these and additional specimens in future studies of Limnodrilus, and the neotype provides a baseline for further revisions of the taxonomy of the L. hoffmeisteri complex.

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DNA barcoding will frequently fail in complicated groups: An example in wild potatoes

Cited by 162 publications

References 109 publications

DNA barcoding of arid wild plants using rbcL gene sequences

DNA barcoding of arid wild plants using rbcL gene sequences

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae)

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